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Subset liger object

Source: R/subsetObject.R
subsetLiger.Rd

This function subsets a liger object with character feature index and any valid cell index. For datasets based on HDF5, the filenames of subset H5 files could only be automatically generated for now. Feature subsetting is based on the intersection of available features from datasets involved by cellIdx, while featureIdx = NULL does not take the intersection (i.e. nothing done on the feature axis).

a ligerDataset object is also allowed for now and meanwhile, setting filename is supported.

Usage

subsetLiger(
  object,
  featureIdx = NULL,
  cellIdx = NULL,
  useSlot = NULL,
  chunkSize = 1000,
  verbose = getOption("ligerVerbose", TRUE),
  newH5 = TRUE,
  returnObject = TRUE,
  ...
)

Arguments

object

A liger or ligerDataset object.

featureIdx

Character vector. Missing or NULL for all features.

cellIdx

Character, logical or numeric index that can subscribe cells. Missing or NULL for all cells.

useSlot

The slot(s) to only consider. Choose one or more from "rawData", "normData" and "scaleData". Default NULL subsets the whole object including analysis result matrices.

chunkSize

Integer. Number of maximum number of cells in each chunk, Default 1000.

verbose

Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.

newH5

Whether to create new H5 files on disk for the subset datasets if involved datasets in the object is HDF5 based. TRUE writes a new ones, FALSE returns in memory data.

returnObject

Logical, whether to return a liger object for result. Default TRUE. FALSE returns a list containing requested values.

...

Arguments passed to subsetLigerDataset

Value

Subset object

See also

subsetLigerDataset

Examples

pbmc.small <- subsetLiger(pbmc, cellIdx = pbmc$nUMI > 200)
#> ℹ Subsetting dataset: "ctrl"
#> ℹ Subsetting dataset: "stim"
#> ✔ Subsetting dataset: "stim" ... done
#> 
#> ℹ Subsetting dataset: "ctrl"

#> ✔ Subsetting dataset: "ctrl" ... done
#> 
pbmc.small <- pbmc[, pbmc$nGene > 50]
#> ℹ Subsetting dataset: "ctrl"
#> ℹ Subsetting dataset: "stim"
#> ✔ Subsetting dataset: "stim" ... done
#> 
#> ℹ Subsetting dataset: "ctrl"

#> ✔ Subsetting dataset: "ctrl" ... done
#>